On 5/2/13 11:01 AM, Dubi wrote:
Dear Gromacs Community,
I m in the situation where I have a trajectory that started in a geometric
position "A" and ended in position "B". If I hit a new mdrun with the
"-append" extension, than the trr output is the old trajectory together with
the new one which starts at position "B". Unfortunately I want the new trr
output to be the old trajectory together with the new one which should start
again at position "A". The new trajectory should differ from the old one,
since I have random seed on.
My question is, how do I get gromacs to do that? Is it enough if I just
don't pass a Checkpoint file, or should I construct a checkpointfile from
the first frame? To get a checkpointfile from the first frame I guess I have
to start a trajectory with 1 timestep - or is there a smarter way?
You can't build a new checkpoint file like that. It sounds to me like you just
need to run a new simulation. Setting gen_seed = -1 generates a random seed for
velocities, but those velocities are then stored in the .tpr file; they are not
re-generated randomly when mdrun begins.
I think what you need to do is just run a new simulation. If you want to append
it to your existing .trr file (for whatever reason), that's what trjcat is for.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
